CS-5630 / CS-6630 Visualization for Data Science Set Visualization - PowerPoint PPT Presentation

CS-5630 / CS-6630 Visualization for Data Science Set Visualization Alexander Lex alex@sci.utah.edu [xkcd]

Design Workshop

item1 : A item2 : A A item3 : A, B item4 : A, C item5 : A, B, C B item6 : B item7 : B, C C item8 : C … Venn diagram

LETTER doi:10.1038/nature11241 The banana ( Musa acuminata ) genome and the evolution of monocotyledonous plants ´lique D’Hont 1 * , France Denoeud 2,3,4 * , Jean-Marc Aury 2 , Franc-Christophe Baurens 1 , Françoise Carreel 1,5 , Olivier Garsmeur 1 , Ange Benjamin Noel 2 , Ste ´phanie Bocs 1 , Gae ¨tan Droc 1 , Mathieu Rouard 6 , Corinne Da Silva 2 , Kamel Jabbari 2,3,4 , Ce ´line Cardi 1 , Julie Poulain 2 , Marle `ne Souquet 1 , Karine Labadie 2 , Cyril Jourda 1 , Juliette Lengelle ´ 1 , Marguerite Rodier-Goud 1 , Adriana Alberti 2 , Maria Bernard 2 , Margot Correa 2 , Saravanaraj Ayyampalayam 7 , Michael R. Mckain 7 , Jim Leebens-Mack 7 , Diane Burgess 8 , Mike Freeling 8 , Didier Mbe ´ 9 , Matthieu Chabannes 5 , Thomas Wicker 10 , Olivier Panaud 11 , Jose Barbosa 11 , ´guie ´-A-Mbe ´guie Eva Hribova 12 , Pat Heslop-Harrison 13 , Re ´my Habas 5 , Ronan Rivallan 1 , Philippe Francois 1 , Claire Poiron 1 , Andrzej Kilian 14 , Dheema Burthia 1 , Christophe Jenny 1 , Fre ´ric Bakry 1 , Spencer Brown 15 , Valentin Guignon 1,6 , Gert Kema 16 , Miguel Dita 19 , ´de Cees Waalwijk 16 , Steeve Joseph 1 , Anne Dievart 1 , Olivier Jaillon 2,3,4 , Julie Leclercq 1 , Xavier Argout 1 , Eric Lyons 17 , Ana Almeida 8 , Mouna Jeridi 1 , Jaroslav Dolezel 12 , Nicolas Roux 6 , Ange-Marie Risterucci 1 , Jean Weissenbach 2,3,4 , Manuel Ruiz 1 , ´tier 18 , Nabila Yahiaoui 1 & Patrick Wincker 2,3,4 Jean-Christophe Glaszmann 1 , Francis Que Bananas ( Musa spp.), including dessert and cooking types, are giant sequence errors. The assembly consisted of 24,425 contigs and 7,513 perennial monocotyledonous herbs of the order Zingiberales, a scaffolds with a total length of 472.2 Mb, which represented 90% of sister group to the well-studied Poales, which include cereals. the estimated DH-Pahang genome size. Ninety per cent of the Bananas are vital for food security in many tropical and subtropical assembly was in 647 scaffolds, and the N50 (the scaffold size above countries and the most popular fruit in industrialized countries 1 . which 50% of the total length of the sequence assembly can be found) The Musa domestication process started some 7,000 years ago in was 1.3 Mb (Supplementary Text and Supplementary Tables 1–3). We Southeast Asia. It involved hybridizations between diverse species anchored 70% of the assembly (332 Mb) along the 11 Musa linkage and subspecies, fostered by human migrations 2 , and selection of groups of the Pahang genetic map. This corresponded to 258 scaffolds and included 98.0% of the scaffolds larger than 1 Mb and 92% of the diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current annotated genes (Supplementary Text, Supplementary Table 4 and production relies on somaclones derived from a single triploid Supplementary Fig. 1). genotype (Cavendish) 1 . Pests and diseases have gradually become We identified 36,542 protein-coding gene models in the Musa adapted, representing an imminent danger for global banana pro- genome (Supplementary Tables 1 and 5). A total of 235 microRNAs duction 3,4 . Here we describe the draft sequence of the 523-megabase from 37 families were identified, including only one of the eight microRNA gene ( MIR ) families found so far solely in Poaceae 8 genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We (Supplementary Tables 6 and 7). detected three rounds of whole-genome duplications in the Musa Viral sequences related to the banana streak virus (BSV) dsDNA lineage, independently of those previously described in the Poales plant pararetrovirus were found to be integrated in the Pahang lineage and the one we detected in the Arecales lineage. This first genome, with 24 loci spanning 10 chromosomes (Supplementary monocotyledon high-continuity whole-genome sequence reported Text and Supplementary Fig. 2). They belonged to a badnavirus Nature 2012 outside Poales represents an essential bridge for comparative phylogenetic group that differed from the endogenous BSV species (eBSV) found in M. balbisiana 9 and most of them formed a new genome analysis in plants. As such, it clarifies commelinid-

[Neale et al., BMC Genome Biology, 2014] [Gibbs et al., Nature, 2004] [D’Hont et al., Nature, 2012] [Wiles et al., BMC Systems Biology]

What are some questions we’d like to ask?

Design Workshop work in groups get to know the data (5 mins) create two (rapid!) prototypes (2x5 mins) Write up your two favorites (5 mins) Upload to “Bonus” Canvas Dropbox by EOD

1. What is the biggest intersection? 2. Which sets make up an intersection? 3. How big is an intersection? 4. Does it work for more than four sets? 5. Does attribute value correlate with intersection Tip: Don’t always try to show all individuals

Venn and Euler Diagrams

Venn vs Euler Euler Diagram Venn Diagram Shows logical relations Shows all possible logical relations between sets May omit empty (even if empty) intersections

Venn Diagrams Venn diagrams for many sets are hard # of intersections is 2 n https://en.wikipedia.org/wiki/Venn_diagram

Area-Proportional Euler Diagrams Problem with Venn: size doesn’t correspond to the data. Creating area-proportional Euler diagrams is hard. Layout criteria: area proportional simple curves (circles are best) makes it easy to identify which sets are participating in intersection Gestalt-principle: good continuation [Alsallakh 2015]

Compare Simple vs Complex Shape Complex Simple

[created with EulerAPE]

? 43 > < 19 19 22 9 5 41 22 44 [created with EulerAPE]

Venn-Euler Pros/Cons Pros Cons Familiar Doesn’t work well for more than 4 sets Intuitive Area proportionality hard to do Work well for 2-4 sets Not well suited to show attributes

Relationships for specific Items No Duplicate Nodes Duplicate Nodes Complex Shapes Simple Shapes [Riche 2010] Notice the Nesting

Sets on top of a fixed layout https://www.youtube.com/watch?v=Ju2hSThmPWA

Sets on top of a fixed layout LineSets Kelp Diagrams [Alper 2011] [Dinkla 2012]

Node-Link Techniques Treat sets as nodes Connect to elements that are in set http://mariandoerk.de/pivotpaths/demo/#/1:0_497686

Showing Pairwise Overlap Doesn’t show higher-order Co-Mutations of genes overlaps Very scalable Can’t show attributes

Set Matrices: OnSet Set membership for each item shown in matrix Comparisons can be made using AND or OR operations Good for many sets and few items https://vimeo.com/213029678#at=0 [Sadana 14]

Linear Diagrams [RODGERS 2015]

Radial Sets Sets are segments on a “circle” Relationships are encoded as ribbons Size of segments encodes size of sets Histograms in segments show degrees https://www.youtube.com/watch?v=UcYRrPqC5A8 [Alsallakh 2013]

UpSet [InfoVis’14] Visualizing Intersecting Sets

1. Efficient visual encoding vs. Set Vis Goals 2. Creating complex slices of a dataset 3. Visualize attributes

Attribute Details [Movie Lens Dataset] Visualizing Intersections Visualizing Properties Element List & Queries

Visualizing Intersections

Universal Set A B C A B C

Must Universal Set Must Not A B C A B C

A B C Cardinality 5 5 17 17 20 7 14 5 10 7 10 7 14 20 7 5

Plotting Attributes

How surprising is the size of an intersection? What’s the distribution of an attribute in an intersection? Additional Plots Deviation Attributes A B C

Drama- Comedy Action- Comedy

Sorting

Which is the biggest intersection? Sort By: Cardinality A B C

Elements & Attributes

How do documentaries compare to adventure movies?

How do documentaries compare to adventure movies?

Applications

R-Version: UpSetR Developed at HMS Some design adaptions

The Banana Chart Redesigned

Other Options http://setviz.net